Description
Hundreds of genes and thousands of interactions turn into an unreadable table in a spreadsheet. Cytoscape draws them as a network instead: each protein is a node, each interaction an edge, and the structure shows itself.
The most useful trick is visual mapping: map expression levels straight onto node color, red for up and green for down, and you can see which part of the network is changing at a glance instead of comparing rows of numbers.
Network visualization:Load molecular interaction networks and pathway data, zoom and pan freely, and use the bird's-eye view to navigate large graphs.
Attribute integration:Attach annotations and expression data to nodes and edges, and drive color, size and shape from them.
NetworkAnalyzer:Compute degree distribution, clustering coefficients and other topology measures to find key nodes.
Rich app ecosystem:Community apps cover bioinformatics, social network analysis, the semantic web and more.
Open source and free:Java-based, runs on Windows, macOS and Linux, free for research and teaching.
The most useful trick is visual mapping: map expression levels straight onto node color, red for up and green for down, and you can see which part of the network is changing at a glance instead of comparing rows of numbers.
Features
Network visualization:Load molecular interaction networks and pathway data, zoom and pan freely, and use the bird's-eye view to navigate large graphs.
Attribute integration:Attach annotations and expression data to nodes and edges, and drive color, size and shape from them.
NetworkAnalyzer:Compute degree distribution, clustering coefficients and other topology measures to find key nodes.
Rich app ecosystem:Community apps cover bioinformatics, social network analysis, the semantic web and more.
Open source and free:Java-based, runs on Windows, macOS and Linux, free for research and teaching.
